3D microscopy represents a powerful new cell analysis tool for early detection and diagnosis of cancer, but its future use may be limited because methods for preparation of samples are cumbersome, inefficient, labor intensive and generally imprecise. Current methods for cytological sample collection are manual and distributed in nature through various physicians' office laboratories and local hospitals, with the actual analysis being centralized at regional clinical laboratories. Among the cytological specimens are sputum, gynecological and colorectal scrapes, fine needle aspirates, urinary tract, and gastrointestinal samples. We propose the development of a new automated system that will transform these difficult and messy clinical specimens into an optimal format for 3D microscopy morphological and molecular analysis. The model and method we propose is comprised of three sequential steps. First, at the distributed site, an automated sample processor dissociates and fixes cells and debris for shipment in an automation compatible canister. Second, after shipment to a centralized clinical laboratory, the specimen canisters are loaded into an automatic processor that performs cleanup (debris removal), specimen/assay specific staining (and counterstaining), and finally embedding of cells of interest in glass microcapillary tubes (about 50 mu m ID), with cells being spaced at regular intervals (about 200 mu m) within a tube. This preparation format is uniquely suited for integration with multiple 3D imaging platforms for true 3D volumetric assessment of cell morphology and molecular probe and/or stain density distribution. The proposed system also enables use of cytometric flow sorting for enrichment of cells of interest at an intermediate stage of the sample preparation process. The potential impact to improved human health through rapid diagnostic screening will be illustrated using a high impact emerging technology, optical tomography. In summary, the aim of the proposed project is to develop, design, and build a complete sample processing system that automates the process of sample cleanup, assay specific staining, and mounting of cells into glass microcapillary tubes, and a tube positioning and rotation scanner mechanism for 3D microscopy analysis of cell morphology for the early detection of cancer.